public class SnrScore extends Object
Constructor and Description |
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SnrScore(AaOccurrence aaOccurrence)
Constructor.
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Modifier and Type | Method and Description |
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double |
getScore(Peptide peptide,
MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Returns the score.
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double |
getScore(Peptide peptide,
MSnSpectrum spectrum,
ArrayList<IonMatch> ionMatchesList)
Returns the score.
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double |
getScore(Peptide peptide,
MSnSpectrum spectrum,
HashMap<Double,ArrayList<IonMatch>> ionMatches)
Returns the score.
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public SnrScore(AaOccurrence aaOccurrence)
aaOccurrence
- the amino acid occurrence in the databasepublic double getScore(Peptide peptide, MSnSpectrum spectrum, AnnotationSettings annotationSettings, SpecificAnnotationSettings specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator) throws InterruptedException, org.apache.commons.math.MathException
peptide
- the peptide of interestspectrum
- the spectrum of interestannotationSettings
- the general spectrum annotation settingsspecificAnnotationSettings
- the annotation settings specific to
this PSMpeptideSpectrumAnnotator
- the spectrum annotator to useInterruptedException
- exception thrown if a threading
error occursorg.apache.commons.math.MathException
- exception if an exception
occurs when calculating logspublic double getScore(Peptide peptide, MSnSpectrum spectrum, ArrayList<IonMatch> ionMatchesList) throws InterruptedException, org.apache.commons.math.MathException
peptide
- the peptide of interestspectrum
- the spectrum of interestionMatchesList
- the ion matches obtained from spectrum annotationInterruptedException
- exception thrown if a threading
error occursorg.apache.commons.math.MathException
- exception if an exception
occurs when calculating logspublic double getScore(Peptide peptide, MSnSpectrum spectrum, HashMap<Double,ArrayList<IonMatch>> ionMatches) throws InterruptedException, org.apache.commons.math.MathException
peptide
- the peptide of interestspectrum
- the spectrum of interestionMatches
- the ion matches obtained from spectrum annotation
indexed by mzInterruptedException
- exception thrown if a threading
error occursorg.apache.commons.math.MathException
- exception if an exception
occurs when calculating logsCopyright © 2018. All rights reserved.